Capability to use arbitrary Runge-Kutta methods in SharpClaw.  Untested.
Arbitrary Runge-Kutta methods working in SharpClaw.
Spatial splitting with embedded RK methods.
switch mask logic

1 is use b method, 0 is use b_hat
Add Shu-Osher shock-sine nteraction problem.
Convert NaNs to zeros.
Fix bug in ascii.py.
Merge branch 'master' into runge_kutta

* master: (163 commits)
  Updat README.md to reflect apps -> examples name change in 04054b81ae
  Remove broken and unused inlinelimiter.
  Compile shallow water on sphere fortran source in correct directory.
  Fixing incorrect sense of division in inlinelimiter.f90
  write initial aux if write_aux_always is set.
  Remove two unnecessary lines in Makefile.
  Add self-contained Makefile in examples/shallow_sphere.
  removed most obvious unnecessary Makefiles
  fixed bare pyclaw import
  fix unnecessary import pyclaw
  deleted duplicated setup.py
  Standardize example names and import into examples.x namespace.
  Update examples to work with gallery scripts.
  Rename apps/ directory to examples/.
  Add elasticity example in fvmbook/chap22/inclusion.
  Undo my modification to the acoustics IO test.
  docstring inheritance
  Fix bugs.
  Use pythonic names for io functions.
  small path fixes
  ...

Conflicts:
	src/pyclaw/io/ascii.py
	src/pyclaw/sharpclaw/solver.py
Move shocksine example to examples directory.
Remove mask capability.
Update shocksine example.
Shocksine test.
Working shocksine test.
Loosen test tolerance.
Merge pull request #321 from ketch/runge_kutta

Use any Runge-Kutta method in SharpClaw